Sunday, March 22, 2015

For the next two weeks, I’ll conduct a new test to measure the effect of simvastatin on my Brain Reaction Time.

Two or three Kirkland fish oil pills taken daily make me score higher on Seth Robert’s Brain Reaction Time test. After six months of self-testing, the effect is pretty robust, as you can see from this simple T-test:

What causes the effect? I have some guesses related to role that Omega-3 fats play in brain nutrition, but are there other ways to get similar effects? I’ve already disproven many of the obvious other candidates (sleep, alcohol, vitamin D), but several fellow quantified-selfers have suggested I look also at statin drugs, which besides lowering cholesterol, also seem to benefit the brain. Mark Drangsholt, who studied this extensively on himself, says 2-3 weeks of treatment helped him reduce or eliminate brain fog.

So I’m going to try the same thing: for the next two weeks, I’ll take 20mg of simvastatin daily while I continue to test my BRT for changes. I’ve taken no fish oil for the past two weeks (and as predicted, my BRT averages have declined), so this should be a “clean test”.

Monday, March 16, 2015

As suspected, there was a glitch in my latest uBiome results. Apparently a server hiccupped, so the scientists there recomputed my sample and sure enough, the new data is much more believable. Here is the single chart summary of all four of the uBiome tests results I’ve received so far:

You can see a number of changes, but what’s exciting about this one is that it’s the first sample where I was deliberately trying to test something: the effect on my gut of taking potato starch to hack my sleep.

A few details about this sample:

Taken on Jan 19th, almost exactly 3 months after my Oct 17th sample.

During the 94 days between samples, I had 31 days where I took a dose of potato starch, a total of about 80 tablespoons.

I had been taking 1 T daily, an hour before bedtime, for a week before this sample.

To analyze my results, I first popped into my publicly-available uBiome utilities, using the data I had already downloaded from the site. If you want to follow along at home, here are some of the commands I typed.

The units are all uBiome’s “count_norm” field, which you can think of as, roughly, a percentage (a fraction of one million). Items in italics are “good”.

I'll have much more to say as I analyze this for a future post, but so far I'm thinking that no, potato starch didn't wreck my gut. The benefits in better sleep appear to come at little or no major cost to the rest of my gut flora. What do you think?

Here’s a comparison chart showing all four of my uBiome submissions:
In a word: argh!

If the January 19th sample had been my first and only uBiome test, I’d be tempted to read a lot into this. After all, it appears that my levels of proteobacteria are way outside the norm. That’s not all: look at some other oddities about this one:

Lots of prevotella (almost 3% of the sample), a species that didn’t appear in any of my previous samples, and a bit worrisome for a meat-eater like me.

No more Clostridum, either. Commonly thought of as a pathogen, it may be good to get rid of this, but why did it disappear?

All of these massive changes in the span of only three months? Not impossible – the human gut can change pretty quickly under the right circumstances. But you’d expect something different about my environment, eating habits, and certainly my health.

But here’s the thing: I don’t notice a single difference in my health or well-being over this time period. Same sleep, same weight, same general mood. Diet, bowel movements, skin – like everyone, I see minor day-to-day variations, but absolutely nothing about me is different enough to be noteworthy.

On the other hand, there are a few oddities in the sample itself. First, uBiome warned that their first run had too low levels of bacteria; the ones you see above came after they ran the sample again under more amplified settings. Second, I used an older kit, one that had been lying around the house for about a year. Finally, I also ran into trouble with the mail, so it sat around at the post office for several more weeks than normal. Shouldn’t really matter, but still…

Soooo, my bottom line is that I’m just not going to read much into this sample. I’m waiting on my next submission, one that was sent a few weeks after this one, and hopefully that will give me a much better picture.

The takeaway for you? Don’t read much into a single uBiome test. The science is too new, and there are so many other factors that go into the results. My advice: send in multiple kits, spread over several weeks or months, before jumping to conclusions.

Wednesday, March 11, 2015

What if you were in New York City and somebody gave you a list of the GPS coordinates for every coffee shop in the area. If you knew nothing else, would that information be useful or distracting? The answer depends on what you’re trying to do. If you just want to know, roughly, where people congregate, then it's probably a nice guide. But if you're lost and you need to get across town, then that information may be worse than useless: without knowing the roads or subways, you may end up in the Hudson River.

That’s how I look at my uBiome test results and the wonderful and incredibly detailed analysis done for me by Dr. Grace Liu, who I consider to be one of the world’s best experts about the gut microbiome. Please read her blog, and listen to her Gut Guardians podcast, where she goes into far more detail, but here’s her conclusion about my results:

Unfortunately after amputating over 1/3 of his gut species, many of the phylogenetic core are depleted. The initial levels were awesome but after a high dose of single source of 'fiber', many on re-testing were gone and dramatically diminished numbers.

She’s referring to my “sleep hacking” experiment using raw potato starch to improve my sleep. Another way to put this (in my own words):

Raw potato starch — which is not in any ancestral diet — is bad for health. It may temporarily improve sleep by feeding gut bacteria responsible for the production of most sleep hormones, but it also crowds out other, more important organisms, and opens the door for pathogens that can cause far more trouble.

Sounds pretty dangerous, and of course I stopped all potato starch experimentation immediately after her warning.

Here’s my summary of the uBiome test results that drove her conclusion (pulled straight from my publicly available data)

Organism

May

Jun

Oct

Rank

Faecalibacterium prausnitzii

99571

62316

5790

species

Roseburia

13554

11157

7825

genus

Christensenellaceae

82585

39713

40290

family

Christensenella

269

NA

38

genus

Akkermansia

30960

19654

7648

genus

Bifidobacteria Longum

32

NA

1858

species

Bifidobacterium

8473

6532

58747

genus

B. Longum as % of total Bifido

0.38%

NA

3.16%

Clostridium

35012

41679

71326

genus

C. botulinum

NA

25

species

C. clostridioforme

28902

35372

15170

species

C. baratii

1223

NA

5588

species

The units are all uBiome’s “count_norm” field, which you can think of as, roughly, a percentage (a fraction of one million). Items in italics are "good".

Her analysis compares only my May and October samples (she dismisses my Jun result as an anomaly) but what if that's not fair? True, there are some issues with the data for June (for some reason, uBiome computed a much smaller sample that time and you can see from the chart that a few items are missing), but it’s still data, and we can’t be sure that the other samples are any more (or less) accurate. To use the New York coffee shop analogy, when you have almost no information to begin with, are you better or worse off when you drop some data points? The answer is that it depends on what you’re trying to accomplish.

Dr. Liu is alarmed at the drop in some key species between May and October, a fact she attributes to my potato starch experiment. But all of those numbers were already dropping in June. The five months pre-potato starch between May and October coincided with seasonal changes (late Spring to Summer to early Fall), lots of travel, multiple camping trips, and of course the normal dietary shifts that happen as I gained access to the freshly-harvested fruits and vegetables of Summer. Was a week of a couple tablespoons of potato starch really the most important change?

In fact, in this table the only species that reversed course after the initial May-June samples and October were the bifidobacterium (often associated with good health and sleep, and up by a LOT) and the clostridioforme (a potential pathogen, down by a little).

I'm pretty healthy, thankfully, and there are no particular disorders I'd like to treat. Like anyone, I want to feel even better, but in my self-experimentation I certainly don't want to risk falling into some terrible dysbiosis or worse. Potato starch appeared on the surface to help -- the improvement in sleep seemed promising -- but I take Dr. Liu's advice and expertise seriously, so I stopped until I can see more uBiome results. I submitted one sample right after my last experiment, and another a few weeks after that. If potato starch really wrecked my gut, then I'll expect the new samples will show considerable worsening across the board. But if not, then, well, maybe it's okay to continue the experiment. Either way, I'll be taking her bionic fiber advice seriously.

To go back to the New York coffee shop analogy, I think we have to respect how very, very little is known about the terrain around us. When you know absolutely nothing about the critically important gut environment, then a tool like uBiome is such a precious gift of information that it's tempting to use it for much more than it is. We'll need much more data, from many more people, before we can use this information to get across town without falling in the river.

About Me

Years building software and marketing teams at Apple, Microsoft, and startups in the US, Japan, and China have given me an awareness of how little I know, but at least I try to write it down before I forget.